preprocess_molgan_database

utils/preprocess-molgan-database-plugin/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/mm/utils/preprocess_molgan_database/__init__.py]

utils/preprocess-molgan-database-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/preprocess-molgan-database-plugin/.gitignore

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+poetry.lock

utils/preprocess-molgan-database-plugin/CHANGELOG.md

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+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

utils/preprocess-molgan-database-plugin/Dockerfile

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+# docker build -f Dockerfile -t polusai/molgan-tool:0.1.0 .
+FROM condaforge/mambaforge
+# NOT mambaforge-pypy3 (rdkit is incompatible with pypy)
+
+# RDKIT logging
+ENV RDKIT_ERROR_LOGGING="OFF"
+
+RUN apt-get update && apt-get install -y wget git
+
+# Clone MolGAN
+RUN git clone https://github.com/ndonyapour/MolGAN.git
+
+# Build and install python bindings
+# MolGAN was initially implemented using TensorFlow v1, and TensorFlow version 2 offers support
+# for v1 functionalities. However, it's important to mention that the current patch for upgrading
+# to v2 is not truly upgrading v1 API to v2 API, but calling legacy v1 API from v2 package via
+# "tf.compat.v1". Essentially, it’s still v1.certain. Truely upgrade to v2 requires rewriting most
+# functions of MolGAN, including model creation, data processing, and training.
+
+RUN mamba install -c conda-forge rdkit "tensorflow<2.13" numpy scikit-learn xorg-libxrender
+
+# Make sure rdkit is activated
+RUN python -c "import rdkit"
+
+# Train a Model
+WORKDIR /MolGAN
+
+# Download the gdb9 database
+RUN bash data/download_dataset.sh data/gdb9.sdf data/NP_score.pkl.gz data/SA_score.pkl.gz
+
+# Download the pretrained model
+RUN wget -nv --no-clobber https://huggingface.co/ndonyapour/MolGAN/resolve/main/MolGAN_model.tar.gz && tar xvzf MolGAN_model.tar.gz
+RUN mv MolGAN_model trained_models
+RUN  wget -nv --no-clobber https://huggingface.co/ndonyapour/MolGAN/resolve/main/data.pkl -O data/data.pkl
+ADD Dockerfile .

utils/preprocess-molgan-database-plugin/README.md

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+# preprocess_molgan_database (0.1.0)
+
+MolGAN tool for generating small molecules
+
+## Options
+
+This plugin takes 2 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_sdf_path | Path to the input file, Type: File, File type: input, Accepted formats: sdf | Input | File | File |
+| output_data_path | Path to the output data file, Type: string, File type: output, Accepted formats: pkl, Example file: https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_model_support_vector_machine.pkl | Input | string | string |
+| output_data_path | Path to the output data file | Output | File | File |

utils/preprocess-molgan-database-plugin/VERSION

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+0.1.0

utils/preprocess-molgan-database-plugin/ict.yml

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+specVersion: "0.1.0"
+name: preprocess_molgan_database
+version: 0.1.0
+container: preprocess-molgan-database-plugin
+entrypoint:
+title: preprocess_molgan_database
+description: MolGAN tool for generating small molecules
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_sdf_path
+    required: true
+    description: Path to the input file, Type File, File type input, Accepted formats sdf
+    type: File
+    defaultValue: system.sdf
+    format:
+      uri: edam:format_3814
+  - name: output_data_path
+    required: true
+    description: Path to the output data file, Type string, File type output, Accepted formats pkl, Example file https//github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_model_support_vector_machine.pkl
+    type: string
+    defaultValue: system.pkl
+    format:
+      uri: edam:format_3653
+outputs:
+  - name: output_data_path
+    required: true
+    description: Path to the output data file
+    type: File
+    format:
+      uri: edam:format_3653
+ui:
+  - key: inputs.input_sdf_path
+    title: "input_sdf_path: "
+    description: "Path to the input file, Type File, File type input, Accepted formats sdf"
+    type: File
+  - key: inputs.output_data_path
+    title: "output_data_path: "
+    description: "Path to the output data file, Type string, File type output, Accepted formats pkl, Example file https//github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_model_support_vector_machine.pkl"
+    type: string

utils/preprocess-molgan-database-plugin/preprocess_molgan_database_0.1.0.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: MolGAN tool for generating small molecules
+
+baseCommand: ["python", "/MolGAN/utils/sparse_molecular_dataset.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull:  polusai/molgan-tool@sha256:e008e74170be12dcf50a936a417b8c330ccdebf7fe17abaa8fa2689dac210725
+
+inputs:
+  input_sdf_path:
+    label: Path to the input file
+    doc: |-
+      Path to the input file
+      Type: File
+      File type: input
+      Accepted formats: sdf
+    type: File
+    format: edam:format_3814 # sdf
+    inputBinding:
+      prefix: --input_sdf_path
+
+  output_data_path:
+    label: Path to the output data file
+    doc: |-
+      Path to the output data file
+      Type: string
+      File type: output
+      Accepted formats: pkl
+      Example file: https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/classification/ref_output_model_support_vector_machine.pkl
+    type: string
+    format: edam:format_3653
+    inputBinding:
+      prefix: --output_data_path
+    default: system.pkl
+
+outputs:
+  output_data_path:
+    label: Path to the output data file
+    doc: |-
+      Path to the output data file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_data_path)
+    format: edam:format_3653 # sdf
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/preprocess-molgan-database-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-preprocess-molgan-database"
+version = "0.1.0"
+description = "MolGAN tool for generating small molecules"
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+cwl-utils = "0.33"
+cwltool = "3.1.20240404144621"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

utils/preprocess-molgan-database-plugin/tests/__init__.py

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+"""Tests for preprocess_molgan_database."""

utils/preprocess-molgan-database-plugin/tests/gdb9_5.sdf

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+gdb_1
+     RDKit          3D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+   -0.0127    1.0858    0.0080 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$$$$
+gdb_2
+     RDKit          3D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+   -0.0404    1.0241    0.0626 N   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$$$$
+gdb_3
+     RDKit          3D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+   -0.0344    0.9775    0.0076 O   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$$$$
+gdb_4
+     RDKit          3D
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+    0.5995    0.0000    1.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5995    0.0000    1.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  3  0
+M  END
+$$$$
+gdb_5
+     RDKit          3D
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+   -0.0133    1.1325    0.0083 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0023   -0.0192    0.0019 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  3  0
+M  END
+$$$$

utils/preprocess-molgan-database-plugin/tests/test_preprocess_molgan_database.py

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+"""Tests for preprocess_molgan_database."""
+import sys
+from pathlib import Path
+
+current_dir = Path(__file__).resolve().parent
+target_dir = current_dir.parent.parent.parent / "cwl_utils"
+sys.path.append(str(target_dir))
+
+from cwl_utilities import call_cwltool  # noqa: E402
+from cwl_utilities import create_input_yaml  # noqa: E402
+from cwl_utilities import parse_cwl_arguments  # noqa: E402
+
+
+def test_preprocess_molgan_database() -> None:
+    """Test preprocess_molgan_database."""
+    cwl_file = Path("preprocess_molgan_database_0.1.0.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+    file_path_str = "gdb9_5.sdf"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["input_sdf_path"]["path"] = file_path
+    input_yaml_path = Path("preprocess_molgan_database_0.1.0.yml")
+
+    create_input_yaml(input_to_props, input_yaml_path)
+    call_cwltool(cwl_file, input_yaml_path)
+    assert Path("system.pkl").exists()